"They physically harmed us. Some of the passengers onboard, they tried to complain and speak about just their problems. They just punched [them] ... and, you know, fall down on the ground," he said.

Mr Morrison released a statement this morning, saying he would not confirm specific operations but, "the Government rejects any allegation of inappropriate behaviour by our Navy or customs and border protection personnel in the conduct of their duties".

"Smugglers and their clients have strong motivations for seeking to discredit the activities of Australia's border protection operations in an attempt to undermine public support for the Government's strong border policies."

Earlier this month, Mr Morrison confirmed Australian sailors were no longer personally liable for what is done under Operation Sovereign Borders.

Territorial breaches 'unlikely unintentional'

Meanwhile, a former Indonesian general and current member of Indonesia's foreign affairs commission says it is impossible that Australian Navy ships ended up in Indonesian waters without intending to, as Mr Morrison and his border protection chief have claimed.

Human Rights Watch report

Mr Morrison said in a briefing last Friday that the Australian Government had apologised to Indonesia after admitting vessels operating under its border protection policy had "inadvertently" breached Indonesian territorial sovereignty "on several occasions".

He said he was told last Wednesday that "border protection command assets had in the conduct of maritime operations associated with Operation Sovereign Borders inadvertently entered Indonesian territorial waters on several occasions" and blamed the incursions on "positional errors".

An inquiry into the incident has been given three weeks to report back.

Lieutenant General Angus Campbell, the commander of Operation Sovereign Borders, said that although an investigation had been launched into the breaches, he was confident they were unintentional.

"I believe our people were acting in good faith at all times," he said of the incursions, adding that the agencies involved in Operation Sovereign Borders regretted "any affront to Indonesia these events may have caused".

However, Tubagus Hasanuddin said experience and training told him that the incursions were unlikely to have been unintentional.

"I studied in Australia - in the military academy. The Australian Navy doesn't have wooden boats, they have warships equipped with modern technology," he said.

"They should have known which part of the water is Indonesia and which is not."